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0.86
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0.74
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0.67
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0.68
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0.67
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0.59
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0.58
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0.61
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0.62
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0.60
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0.74
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0.82
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0.80
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0.65
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-3.377
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0.62
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-1.543
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0.692
0.675
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3.450
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5.494
0.652
1.774
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-3.227
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-4.069
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-3.639
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-2.172
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4.982
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6.015
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6.016
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6.087
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1.348
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6.287
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0.806
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3.423
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2.262
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4.600
2.559
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5.448
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3.010
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5.493
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4.840
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3.136
5.153
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0.439
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1.927
-1.218
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3.981
-0.108
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5.781
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4
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7.014
9.080
5.134
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4
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8.220
7.021
6.070
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6.126
7.885
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4
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6.356
6.970
8.210
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4
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5.478
7.258
9.403
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4
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4.127
6.768
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6.030
6.605
10.624
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4
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6.122
7.559
11.695
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4
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5.089
5.505
10.957
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4
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3.784
5.853
10.253
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4
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4
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3.102
4.638
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4
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3.634
3.533
9.219
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4
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0.54
2.846
2.553
8.937
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4
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1.612
3.060
9.342
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4
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0.51
0.330
2.460
9.297
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4
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4
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0.028
1.338
8.899
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-0.651
3.304
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4
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-0.426
4.586
10.289
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-1.486
5.282
10.737
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0.788
5.151
10.336
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1.756
4.342
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7.390
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6.152
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5.471
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6.218
10.407
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5.472
4.532
10.625
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4
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4.972
5.493
11.997
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3.133
6.363
10.942
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4
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4.692
3.474
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4
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-1.585
2.936
9.775
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4
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-1.346
6.214
11.101
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6.606
7.123
13.169
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1
5
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6.644
8.333
14.021
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6.278
13.032
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13.664
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14.678
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16.935
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17.876
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15.335
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5.266
14.664
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14.601
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15.170
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3.760
13.871
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3.083
13.249
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1.994
12.540
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3.530
13.350
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4.629
14.091
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15.618
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15.213
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17.243
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5.141
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15.265
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1.680
12.472
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1.482
12.072
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3.037
12.807
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3.168
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14.278
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7.365
19.459
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4.192
8.531
20.165
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4.123
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19.744
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19.695
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20.043
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8.264
20.387
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19.409
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21.750
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8.310
22.581
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6.214
21.488
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6.128
20.028
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5.031
19.396
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0.926
4.722
19.560
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1.399
3.680
18.962
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0.257
3.229
18.291
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0.072
2.109
17.443
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0.890
1.254
17.110
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2.034
16.988
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0.66
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2.920
17.303
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0.79
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2.671
16.768
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3.976
18.101
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4.068
18.556
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1.362
9.270
19.205
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1.807
9.010
20.907
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9.157
20.399
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0.751
7.648
22.219
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0.152
5.533
21.728
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5.973
22.075
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5.968
19.959
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1.492
5.344
20.207
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1.251
16.393
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1.872
16.164
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3.281
16.967
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8.773
24.086
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1.61
-1.646
9.932
24.441
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0.676
8.889
24.172
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7.519
24.998
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6.250
24.397
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5.107
25.300
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3.935
24.479
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0.021
5.202
25.936
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0.044
4.716
27.289
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0.829
4.352
25.091
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3.289
24.662
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0.330
2.550
23.478
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0.939
3.023
22.368
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1.355
2.162
21.496
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0.978
0.952
22.089
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1.151
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21.633
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1.701
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20.601
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0.620
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22.535
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0.45
0.001
-0.980
23.724
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-2.007
24.436
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0.270
24.164
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0.345
1.184
23.305
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6.051
23.638
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6.238
23.961
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5.046
26.048
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0.406
6.178
25.900
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1.234
4.882
24.212
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1.593
3.991
25.687
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2.649
25.467
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1.069
4.097
22.218
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0.702
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22.273
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24.100
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-1.841
25.311
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5.053
28.389
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5.036
27.737
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6.237
29.163
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3.754
29.336
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2.556
28.792
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0.924
2.175
29.482
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1.721
1.281
28.643
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1.743
3.437
29.792
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3.634
31.211
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3.257
3.097
29.294
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3.145
1.593
28.675
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3.649
1.579
27.279
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0.60
3.719
2.579
26.359
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0.58
4.156
2.280
25.184
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0.63
4.415
0.916
25.317
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0.67
4.904
-0.042
24.425
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1
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0.68
5.231
0.241
23.165
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0.73
5.037
-1.300
24.879
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8
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0.78
4.708
-1.602
26.137
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8
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1
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0.79
4.235
-0.774
27.065
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8
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0.70
4.111
0.480
26.586
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0.67
-0.254
2.718
27.723
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-1.107
1.748
28.914
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0.688
1.641
30.426
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1.170
4.352
29.301
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0.849
3.739
31.494
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3.685
3.838
28.492
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3.962
3.141
30.192
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3.695
0.712
29.267
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3.409
3.594
26.597
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0.73
5.580
-0.488
22.558
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23.735
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24.735
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23.199
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22.078
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21.692
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21.452
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20.214
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21.960
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19.391
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20.441
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19.923
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21.464
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23.942
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22.194
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22.716
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20.841
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20.276
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21.342
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-4.205
21.217
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-3.685
22.099
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20.689
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19.761
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19.251
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19.289
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0.229
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19.812
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-9.487
23.542
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2
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22.370
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22.874
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20.223
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19.294
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-6.357
20.160
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-5.215
21.877
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2
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-2.459
19.588
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2
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3.148
-3.785
18.523
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2
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1.943
-5.920
18.562
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2
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-7.075
19.462
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2
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-5.501
-7.705
19.740
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3
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-6.903
-7.959
20.143
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3
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18.505
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3
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-6.104
19.645
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3
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-5.230
20.650
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3
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-6.266
-3.888
20.068
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3
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-5.176
-2.974
19.899
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3
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18.740
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3
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-3.515
18.847
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3
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-3.273
17.732
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3
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-5.278
-2.326
18.619
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3
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-3.912
-2.146
18.111
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3
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0.83
-3.470
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17.806
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3
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1.09
-4.260
0.075
17.771
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3
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0.81
-2.145
-0.699
17.542
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3
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0.56
-1.297
-1.735
17.579
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3
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0.55
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17.335
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3
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-3.051
17.887
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3
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0.42
-3.065
-3.202
18.127
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3
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21.412
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3
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21.113
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3
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-3.436
20.733
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3
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18.494
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3
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-5.382
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17.140
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3
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-2.724
17.049
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3
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18.758
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3
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0.333
-0.601
17.124
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1
3
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0.43
0.647
-2.305
17.366
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11
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1
3
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0.45
-1.090
-3.891
18.003
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1
3
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0.46
-3.461
-4.194
18.287
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11
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1
3
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0.66
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-4.080
17.980
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12
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P
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1
4
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P
1.48
-10.757
-3.683
18.648
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4
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O
1.65
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17.676
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4
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0.57
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-3.234
16.623
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4
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O
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-3.729
15.554
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12
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4
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0.65
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-2.793
14.372
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12
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4
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0.66
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-1.672
14.590
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12
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4
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O
0.63
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-3.510
13.139
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4
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C
0.63
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-3.283
12.080
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12
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4
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O
0.61
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-2.965
12.799
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12
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DG
1
4
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C
0.61
-6.697
-1.624
13.515
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12
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DG
1
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C
0.61
-5.325
-1.366
13.991
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N9
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12
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N9
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1
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N
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-4.439
-2.225
14.518
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12
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C8
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1
4
1.00
1
C
0.64
-3.257
-1.790
14.788
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N7
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12
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N7
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1
4
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1
N
0.60
-3.352
-0.456
14.393
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12
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C5
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1
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1.00
1
C
0.58
-2.377
0.571
14.433
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12
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C6
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1
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1.00
1
C
0.59
-1.212
0.497
14.816
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12
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O6
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1
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1.00
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O
0.55
-2.871
1.775
13.951
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12
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N1
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1
4
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1
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0.54
-4.164
1.964
13.474
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12
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C2
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1
4
1.00
1
C
0.53
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3.192
13.038
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12
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N2
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1
4
1.00
1
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0.55
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0.993
13.432
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12
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N3
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1
4
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1
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0.58
-4.619
-0.183
13.904
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12
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1
4
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C
0.88
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-4.689
15.247
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12
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4
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0.96
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-3.852
15.889
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12
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1
4
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0.65
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-2.448
14.202
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12
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1
4
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0.65
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-4.537
13.346
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12
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H3'
DG
1
4
1.00
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H
0.61
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-3.640
13.117
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12
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1
4
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1
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0.59
-6.748
-2.847
11.760
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12
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1
4
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0.59
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-0.837
12.838
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12
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H1'
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1
4
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0.70
-4.718
-3.248
14.700
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12
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1
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1
H
0.57
-2.347
2.586
14.240
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12
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1
4
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1
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0.53
-5.412
3.369
12.683
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12
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1
4
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1
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0.67
-8.821
-3.866
10.598
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5
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1.46
-9.983
-3.502
9.757
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5
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1.56
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-5.283
10.717
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5
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0.81
-7.548
-3.010
10.106
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5
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-7.289
-2.809
8.715
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5
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-7.898
-1.500
8.209
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5
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-7.543
-0.418
9.094
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5
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-7.347
-1.173
6.836
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5
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0.40
-8.418
-0.976
5.905
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5
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O
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-6.543
0.105
6.984
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5
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0.46
-6.672
0.531
8.428
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5
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0.48
-5.374
0.590
9.085
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1
5
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0.45
-4.577
1.734
9.132
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13
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1
5
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1
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0.45
-4.913
2.770
8.563
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13
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1
5
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O
0.47
-3.413
1.651
9.850
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13
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1
5
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0.52
-3.085
0.502
10.475
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13
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1
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1
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0.55
-1.951
0.432
11.173
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13
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N4
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1
5
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1
N
0.59
-3.949
-0.642
10.392
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13
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1
5
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1
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0.56
-5.065
-0.490
9.663
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13
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1
5
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0.67
-7.713
-3.639
8.149
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5
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0.71
-6.211
-2.790
8.555
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5
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0.55
-8.991
-1.591
8.154
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5
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-6.691
-1.977
6.524
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13
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5
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0.41
-5.497
-0.083
6.742
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13
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5
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0.36
-6.945
0.877
6.328
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5
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-7.115
1.430
8.504
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13
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1
5
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0.52
-1.344
1.237
11.230
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13
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H41
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1
5
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1
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0.62
-1.700
-0.424
11.645
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13
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H42
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1
5
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0.68
-3.744
-1.571
10.941
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13
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1
5
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H
0.63
-5.763
-1.258
9.486
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13
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1
5
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1
H
0.92
-8.147
-0.917
4.321
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14
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P
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1
6
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1
P
1.73
-9.443
-1.073
3.623
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14
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1
6
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1
O
1.83
-7.025
-1.830
4.005
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14
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6
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O
0.74
-7.639
0.594
4.116
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14
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6
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O
0.40
-8.555
1.648
3.799
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14
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1
6
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C
0.43
-7.803
2.923
3.446
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14
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DG
1
6
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C
0.47
-6.759
3.146
4.404
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14
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1
6
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O
0.44
-7.194
2.814
2.070
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14
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1
6
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C
0.48
-7.540
3.947
1.253
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14
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1
6
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O
0.48
-5.716
2.745
2.304
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14
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DG
1
6
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1
C
0.46
-5.493
3.036
3.763
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14
ATOM
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DG
1
6
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1
C
0.44
-4.677
2.022
4.379
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N9
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14
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N9
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1
6
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1
N
0.43
-4.793
0.750
4.200
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C8
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14
ATOM
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C8
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1
6
1.00
1
C
0.42
-3.964
-0.047
4.788
B
N7
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14
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N7
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1
6
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1
N
0.43
-3.163
0.875
5.472
B
C5
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14
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C5
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1
6
1.00
1
C
0.47
-2.046
0.671
6.319
B
C6
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14
ATOM
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C6
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1
6
1.00
1
C
0.47
-1.510
-0.388
6.642
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O6
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14
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O6
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1
6
1.00
1
O
0.53
-1.544
1.875
6.789
B
N1
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14
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N1
DG
1
6
1.00
1
N
0.55
-2.049
3.125
6.488
B
C2
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14
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C2
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1
6
1.00
1
C
0.64
-1.423
4.165
7.040
B
N2
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14
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N2
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1
6
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1
N
0.51
-3.101
3.325
5.692
B
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14
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N3
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1
6
1.00
1
N
0.45
-3.605
2.163
5.221
B
C4
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14
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1
6
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1
C
0.65
-9.210
1.835
4.654
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14
ATOM
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DG
1
6
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1
H
0.64
-9.152
1.342
2.946
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14
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1
6
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1
H
0.45
-8.457
3.761
3.451
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14
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DG
1
6
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1
H
0.42
-7.550
1.900
1.601
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DG
14
ATOM
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DG
1
6
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1
H
0.48
-5.348
1.758
2.054
B
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DG
14
ATOM
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DG
1
6
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1
H
0.53
-5.204
3.499
1.711
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DG
14
ATOM
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DG
1
6
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1
H
0.49
-5.008
3.923
3.825
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14
ATOM
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H1'
DG
1
6
1.00
1
H
0.46
-5.569
0.426
3.552
B
H8
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14
ATOM
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H8
DG
1
6
1.00
1
H
0.58
-0.736
1.809
7.386
B
H1
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14
ATOM
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H1
DG
1
6
1.00
1
H
0.69
-0.627
4.015
7.642
B
H21
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14
ATOM
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H21
DG
1
6
1.00
1
H
0.66
-1.745
5.104
6.853
B
H22
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14
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H22
DG
1
6
1.00
1
H
0.50
-8.127
3.746
-0.244
B
P
DG
15
ATOM
B
P
DG
1
7
1.00
1
P
1.49
-8.999
4.901
-0.554
B
OP1
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15
ATOM
B
OP1
DG
1
7
1.00
1
O
1.30
-8.664
2.371
-0.352
B
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15
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1
7
1.00
1
O
0.44
-6.812
3.847
-1.178
B
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15
ATOM
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DG
1
7
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1
O
0.37
-5.516
3.665
-0.609
B
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15
ATOM
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DG
1
7
1.00
1
C
0.38
-4.510
3.148
-1.545
B
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15
ATOM
B
C4'
DG
1
7
1.00
1
C
0.32
-3.379
2.780
-0.750
B
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15
ATOM
B
O4'
DG
1
7
1.00
1
O
0.41
-5.052
1.916
-2.210
B
C3'
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15
ATOM
B
C3'
DG
1
7
1.00
1
C
0.50
-4.620
1.777
-3.574
B
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15
ATOM
B
O3'
DG
1
7
1.00
1
O
0.36
-4.500
0.851
-1.404
B
C2'
DG
15
ATOM
B
C2'
DG
1
7
1.00
1
C
0.32
-3.173
1.411
-0.973
B
C1'
DG
15
ATOM
B
C1'
DG
1
7
1.00
1
C
0.28
-2.620
0.690
0.186
B
N9
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15
ATOM
B
N9
DG
1
7
1.00
1
N
0.27
-3.256
0.238
1.291
B
C8
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15
ATOM
B
C8
DG
1
7
1.00
1
C
0.31
-2.572
-0.460
2.137
B
N7
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15
ATOM
B
N7
DG
1
7
1.00
1
N
0.31
-1.311
-0.482
1.533
B
C5
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15
ATOM
B
C5
DG
1
7
1.00
1
C
0.36
-0.100
-1.095
1.963
B
C6
DG
15
ATOM
B
C6
DG
1
7
1.00
1
C
0.42
0.109
-1.773
2.976
B
O6
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15
ATOM
B
O6
DG
1
7
1.00
1
O
0.36
0.926
-0.867
1.060
B
N1
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15
ATOM
B
N1
DG
1
7
1.00
1
N
0.34
0.822
-0.146
-0.108
B
C2
DG
15
ATOM
B
C2
DG
1
7
1.00
1
C
0.38
1.941
-0.022
-0.822
B
N2
DG
15
ATOM
B
N2
DG
1
7
1.00
1
N
0.32
-0.309
0.430
-0.525
B
N3
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15
ATOM
B
N3
DG
1
7
1.00
1
N
0.29
-1.332
0.226
0.337
B
C4
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15
ATOM
B
C4
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1
7
1.00
1
C
0.32
-5.553
2.886
0.133
B
H5'
DG
15
ATOM
B
H5'
DG
1
7
1.00
1
H
0.40
-5.172
4.598
-0.158
B
H5''
DG
15
ATOM
B
H5''
DG
1
7
1.00
1
H
0.44
-4.223
3.840
-2.278
B
H4'
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15
ATOM
B
H4'
DG
1
7
1.00
1
H
0.42
-6.099
1.869
-2.161
B
H3'
DG
15
ATOM
B
H3'
DG
1
7
1.00
1
H
0.34
-5.123
0.612
-0.525
B
H2'
DG
15
ATOM
B
H2'
DG
1
7
1.00
1
H
0.42
-4.415
0.029
-2.027
B
H2''
DG
15
ATOM
B
H2''
DG
1
7
1.00
1
H
0.35
-2.525
1.375
-1.786
B
H1'
DG
15
ATOM
B
H1'
DG
1
7
1.00
1
H
0.27
-4.310
0.461
1.457
B
H8
DG
15
ATOM
B
H8
DG
1
7
1.00
1
H
0.40
1.817
-1.270
1.303
B
H1
DG
15
ATOM
B
H1
DG
1
7
1.00
1
H
0.41
2.795
-0.456
-0.503
B
H21
DG
15
ATOM
B
H21
DG
1
7
1.00
1
H
0.40
1.935
0.508
-1.682
B
H22
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15
ATOM
B
H22
DG
1
7
1.00
1
H
1.03
-4.602
2.989
-4.644
B
P
DA
16
ATOM
B
P
DA
1
8
1.00
1
P
1.89
-4.185
4.235
-3.962
B
OP1
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16
ATOM
B
OP1
DA
1
8
1.00
1
O
1.91
-5.864
2.950
-5.417
B
OP2
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16
ATOM
B
OP2
DA
1
8
1.00
1
O
0.97
-3.401
2.511
-5.606
B
O5'
DA
16
ATOM
B
O5'
DA
1
8
1.00
1
O
0.85
-2.444
1.575
-5.093
B
C5'
DA
16
ATOM
B
C5'
DA
1
8
1.00
1
C
0.88
-2.506
0.213
-5.825
B
C4'
DA
16
ATOM
B
C4'
DA
1
8
1.00
1
C
0.78
-1.907
-0.850
-5.018
B
O4'
DA
16
ATOM
B
O4'
DA
1
8
1.00
1
O
0.92
-3.964
-0.156
-6.143
B
C3'
DA
16
ATOM
B
C3'
DA
1
8
1.00
1
C
1.10
-4.163
-0.068
-7.560
B
O3'
DA
16
ATOM
B
O3'
DA
1
8
1.00
1
O
0.85
-4.116
-1.715
-5.692
B
C2'
DA
16
ATOM
B
C2'
DA
1
8
1.00
1
C
0.79
-2.653
-2.101
-5.087
B
C1'
DA
16
ATOM
B
C1'
DA
1
8
1.00
1
C
0.68
-2.797
-2.628
-3.706
B
N9
DA
16
ATOM
B
N9
DA
1
8
1.00
1
N
0.59
-3.770
-2.412
-2.779
B
C8
DA
16
ATOM
B
C8
DA
1
8
1.00
1
C
0.59
-3.627
-2.967
-1.623
B
N7
DA
16
ATOM
B
N7
DA
1
8
1.00
1
N
0.66
-2.414
-3.639
-1.780
B
C5
DA
16
ATOM
B
C5
DA
1
8
1.00
1
C
0.74
-1.661
-4.441
-0.917
B
C6
DA
16
ATOM
B
C6
DA
1
8
1.00
1
C
0.79
-2.036
-4.716
0.332
B
N6
DA
16
ATOM
B
N6
DA
1
8
1.00
1
N
0.81
-0.508
-4.946
-1.389
B
N1
DA
16
ATOM
B
N1
DA
1
8
1.00
1
N
0.82
-0.116
-4.680
-2.637
B
C2
DA
16
ATOM
B
C2
DA
1
8
1.00
1
C
0.79
-0.751
-3.935
-3.538
B
N3
DA
16
ATOM
B
N3
DA
1
8
1.00
1
N
0.70
-1.902
-3.439
-3.042
B
C4
DA
16
ATOM
B
C4
DA
1
8
1.00
1
C
0.71
-2.644
1.447
-4.027
B
H5'
DA
16
ATOM
B
H5'
DA
1
8
1.00
1
H
0.92
-1.457
1.986
-5.205
B
H5''
DA
16
ATOM
B
H5''
DA
1
8
1.00
1
H
1.01
-1.927
0.296
-6.768
B
H4'
DA
16
ATOM
B
H4'
DA
1
8
1.00
1
H
0.88
-4.649
0.660
-5.624
B
H3'
DA
16
ATOM
B
H3'
DA
1
8
1.00
1
H
1.39
-5.091
-0.243
-7.729
B
HO3'
DA
16
ATOM
B
HO3'
DA
1
8
1.00
1
H
0.77
-4.954
-1.912
-4.895
B
H2'
DA
16
ATOM
B
H2'
DA
1
8
1.00
1
H
0.97
-4.382
-2.342
-6.609
B
H2''
DA
16
ATOM
B
H2''
DA
1
8
1.00
1
H
0.88
-1.992
-2.884
-5.703
B
H1'
DA
16
ATOM
B
H1'
DA
1
8
1.00
1
H
0.56
-4.631
-1.785
-2.994
B
H8
DA
16
ATOM
B
H8
DA
1
8
1.00
1
H
0.88
-1.456
-5.302
0.916
B
H61
DA
16
ATOM
B
H61
DA
1
8
1.00
1
H
0.77
-2.900
-4.339
0.695
B
H62
DA
16
ATOM
B
H62
DA
1
8
1.00
1
H
0.89
0.829
-5.121
-2.953
B
H2
DA
16
ATOM
B
H2
DA
1
8
1.00
1
H
0.53
-3.487
4.296
13.074
B
C1
TME
1
HETATM
C
C1
TME
2
1.00
1
C
0.52
-3.677
5.222
11.879
B
C2
TME
1
HETATM
C
C2
TME
2
1.00
1
C
0.52
-2.861
4.714
10.696
B
C3
TME
1
HETATM
C
C3
TME
2
1.00
1
C
0.53
-2.492
3.881
13.059
B
H11
TME
1
HETATM
C
H11
TME
2
1.00
1
H
0.55
-3.617
4.859
13.975
B
H12
TME
1
HETATM
C
H12
TME
2
1.00
1
H
0.53
-3.360
6.221
12.141
B
H21
TME
1
HETATM
C
H21
TME
2
1.00
1
H
0.52
-4.721
5.262
11.609
B
H22
TME
1
HETATM
C
H22
TME
2
1.00
1
H
0.53
-3.339
5.017
9.789
B
H31
TME
1
HETATM
C
H31
TME
2
1.00
1
H
0.53
-2.810
3.639
10.726
B
H32
TME
1
HETATM
C
H32
TME
2
1.00
1
H
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Dooley, P.D.
Zhang, M.
Korbel, G.A.
Nechev, L.V.
Harris, C.M.
Stone, M.P.
Harris, T.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C3 H8
44.096
PROPANE
non-polymer
US
J.AM.CHEM.SOC.
JACSAT
0004
0002-7863
125
62
72
10.1021/ja0207798
12515507
NMR Determination of the Conformation of a Trimethylene Interstrand Cross-Link in an Oligodeoxynucleotide Duplex Containing a 5'-d(GpC) Motif
2003
10.2210/pdb1luh/pdb
pdb_00001luh
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
2427.605
5'-D(*TP*CP*CP*(TME)GP*CP*GP*GP*A)-3'
2
syn
polymer
44.096
PROPANE
1
syn
non-polymer
no
no
(DT)(DC)(DC)(DG)(DC)(DG)(DG)(DA)
TCCGCGGA
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
21.248
1
20
A
1
B
16
19.915
A_DT1:DA16_B
1
29.536
0.102
1.338
-0.752
18.318
1
19
A
2
B
15
6.241
A_DC2:DG15_B
2
21.244
1.340
0.152
-0.543
-52.815
1
19
A
3
B
14
3.073
A_DC3:DG14_B
3
-1.146
0.032
-0.306
0.056
-15.073
A
4
B
13
-38.363
A_DG4:DC13_B
4
53.576
0.631
-0.868
-0.026
16.107
A
5
B
12
-38.598
A_DC5:DG12_B
5
52.672
-0.504
-0.908
-0.041
50.652
1
19
A
6
B
11
3.551
A_DG6:DC11_B
6
-1.397
-0.147
-0.433
-0.027
-19.314
1
19
A
7
B
10
5.416
A_DG7:DC10_B
7
22.218
-1.233
-0.031
-0.452
-21.810
1
20
A
8
B
9
18.911
A_DA8:DT9_B
8
32.032
0.207
1.220
-0.664
4.065
25.423
A
A
1
2
29.328
B
B
16
15
4.037
12.287
0.053
1.246
AA_DT1DC2:DG15DA16_BB
1
4.991
-11.913
21.738
-1.901
1.802
0.393
54.014
A
A
2
3
71.612
B
B
15
14
5.746
50.244
-0.396
-1.428
AA_DC2DC3:DG14DG15_BB
2
12.000
-17.104
16.352
-6.327
1.571
2.945
19.286
A
A
3
4
10.436
B
B
14
13
2.943
3.477
-1.508
0.584
AA_DC3DG4:DC13DG14_BB
3
0.673
-2.020
18.961
0.159
4.808
3.188
18.282
A
A
4
5
31.451
B
B
13
12
3.863
9.509
-0.004
-0.229
AA_DG4DC5:DG12DC13_BB
4
0.265
-0.876
15.630
-6.900
0.185
3.122
18.445
A
A
5
6
12.952
B
B
12
11
3.088
4.117
1.530
0.582
AA_DC5DG6:DC11DG12_BB
5
-0.223
0.703
17.982
-0.357
-4.892
0.336
54.483
A
A
6
7
71.813
B
B
11
10
5.673
50.767
0.409
-1.451
AA_DG6DG7:DC10DC11_BB
6
-11.883
16.809
16.393
-6.216
-1.531
4.046
25.765
A
A
7
8
30.030
B
B
10
9
4.036
12.714
-0.065
1.241
AA_DG7DA8:DT9DC10_BB
7
-5.278
12.468
21.832
-1.994
-1.838
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-02-11
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2002-05-22
REL
REL
TME
PROPANE
Details of the synthesis are described in the journal article.
sample
1
2D NOESY
DQF-COSY
PE-COSY
7.10
ambient
303
K
Further details about the structural refinement including the trimethylene chain can be found in the journal article.
NOE-restrained molecular dynamics; simulated annealing
minimized average structure
2 mM crosslinked duplex, 10 mM sodium phosphate buffer, 0.1 M NaCl, 50 mM EDTA, pH 7.1
99.996 % D2O
2 mM crosslinked duplex, 10 mM sodium phosphate buffer, 0.1 M NaCl, 50 mM EDTA, pH 7.1
90% H2O/10% D2O
Biosym Technologies
processing
Felix
95
B.A.Borgias, T.L.L.James
iterative matrix relaxation
MARDIGRAS
A.T.Brunger
structure solution
X-PLOR
3.1
J.W.Keepers, T.L.James
data analysis
CORMA
3.85
A.T.Brunger
refinement
X-PLOR
3.1
500
Bruker
AMX
TME
1
2
TME
TME
1
B
T
1
n
1
DT
1
A
C
2
n
2
DC
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
4
A
C
5
n
5
DC
5
A
G
6
n
6
DG
6
A
G
7
n
7
DG
7
A
A
8
n
8
DA
8
A
T
9
n
1
DT
9
B
C
10
n
2
DC
10
B
C
11
n
3
DC
11
B
+G
12
n
4
DG
12
B
C
13
n
5
DC
13
B
G
14
n
6
DG
14
B
G
15
n
7
DG
15
B
A
16
n
8
DA
16
B
author_defined_assembly
2
dimeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
DC
3
0.060
SIDE CHAIN
1
B
DC
11
0.062
SIDE CHAIN
1
3.97
0.60
106.00
109.97
A
A
A
O4'
C4'
C3'
DC
DC
DC
2
2
2
N
1
4.36
0.30
108.30
112.66
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
4.48
0.30
108.30
112.78
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
5.10
0.50
113.10
118.20
A
A
A
N7
C8
N9
DG
DG
DG
4
4
4
N
1
-2.80
0.40
106.40
103.60
A
A
A
C8
N9
C4
DG
DG
DG
4
4
4
N
1
2.48
0.30
108.30
110.78
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
2.81
0.40
120.30
123.11
A
A
A
C6
N1
C2
DC
DC
DC
5
5
5
N
1
-7.81
1.20
120.80
112.99
A
A
A
C6
N1
C1'
DC
DC
DC
5
5
5
N
1
3.22
0.30
108.30
111.52
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
-3.74
0.50
104.30
100.56
A
A
A
C5
N7
C8
DG
DG
DG
6
6
6
N
1
6.04
0.50
113.10
119.14
A
A
A
N7
C8
N9
DG
DG
DG
6
6
6
N
1
5.81
0.30
108.30
114.11
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
4.64
0.50
113.10
117.74
A
A
A
N7
C8
N9
DG
DG
DG
7
7
7
N
1
-2.57
0.40
106.40
103.83
A
A
A
C8
N9
C4
DG
DG
DG
7
7
7
N
1
3.81
0.50
113.80
117.61
A
A
A
N7
C8
N9
DA
DA
DA
8
8
8
N
1
-2.58
0.40
105.80
103.22
A
A
A
C8
N9
C4
DA
DA
DA
8
8
8
N
1
3.98
0.60
106.00
109.98
B
B
B
O4'
C4'
C3'
DC
DC
DC
10
10
10
N
1
4.47
0.30
108.30
112.77
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
4.37
0.30
108.30
112.67
B
B
B
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
5.07
0.50
113.10
118.17
B
B
B
N7
C8
N9
DG
DG
DG
12
12
12
N
1
-2.77
0.40
106.40
103.63
B
B
B
C8
N9
C4
DG
DG
DG
12
12
12
N
1
2.48
0.30
108.30
110.78
B
B
B
O4'
C1'
N1
DC
DC
DC
13
13
13
N
1
2.79
0.40
120.30
123.09
B
B
B
C6
N1
C2
DC
DC
DC
13
13
13
N
1
-7.85
1.20
120.80
112.95
B
B
B
C6
N1
C1'
DC
DC
DC
13
13
13
N
1
3.16
0.30
108.30
111.46
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
-3.74
0.50
104.30
100.56
B
B
B
C5
N7
C8
DG
DG
DG
14
14
14
N
1
6.09
0.50
113.10
119.19
B
B
B
N7
C8
N9
DG
DG
DG
14
14
14
N
1
5.78
0.30
108.30
114.08
B
B
B
O4'
C1'
N9
DG
DG
DG
15
15
15
N
1
4.69
0.50
113.10
117.79
B
B
B
N7
C8
N9
DG
DG
DG
15
15
15
N
1
-2.66
0.40
106.40
103.74
B
B
B
C8
N9
C4
DG
DG
DG
15
15
15
N
1
3.76
0.50
113.80
117.56
B
B
B
N7
C8
N9
DA
DA
DA
16
16
16
N
1
-2.53
0.40
105.80
103.27
B
B
B
C8
N9
C4
DA
DA
DA
16
16
16
N
1
A
A
C3'
C2'
DT
DT
1
1
0.081
0.012
1.518
1.599
N
1
A
A
C5
C7
DT
DT
1
1
0.037
0.006
1.496
1.533
N
1
A
A
C2'
C1'
DC
DC
2
2
0.069
0.010
1.519
1.588
N
1
A
A
N1
C6
DC
DC
5
5
-0.105
0.006
1.367
1.262
N
1
A
A
C8
N9
DG
DG
6
6
-0.084
0.007
1.374
1.290
N
1
A
A
C3'
C2'
DG
DG
7
7
-0.071
0.008
1.516
1.445
N
1
A
A
C3'
C2'
DA
DA
8
8
0.112
0.012
1.518
1.630
N
1
A
A
C2'
C1'
DA
DA
8
8
0.111
0.010
1.519
1.630
N
1
B
B
C3'
C2'
DT
DT
9
9
0.081
0.012
1.518
1.599
N
1
B
B
C5
C7
DT
DT
9
9
0.037
0.006
1.496
1.533
N
1
B
B
C2'
C1'
DC
DC
10
10
0.068
0.010
1.519
1.587
N
1
B
B
N1
C6
DC
DC
13
13
-0.104
0.006
1.367
1.263
N
1
B
B
C8
N9
DG
DG
14
14
-0.084
0.007
1.374
1.290
N
1
B
B
C3'
C2'
DG
DG
15
15
-0.071
0.008
1.516
1.445
N
1
B
B
C3'
C2'
DA
DA
16
16
0.112
0.012
1.518
1.630
N
1
B
B
C2'
C1'
DA
DA
16
16
0.111
0.010
1.519
1.630
N
minimized average
SOLUTION NMR STRUCTURE OF SELF-COMPLIMENTARY DUPLEX 5'-D(TCCG*CGGA)2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*
1
N
N
1
N
N
2
N
N
covale
1.488
none
A
DG
4
A
N2
DG
4
1_555
B
TME
1
C
C3
TME
1_555
covale
1.487
none
B
TME
1
C
C1
TME
1_555
B
DG
12
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
DA
16
B
N1
DA
8
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
DA
16
B
N6
DA
8
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
15
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
15
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
15
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
14
B
N1
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
14
B
O6
DG
6
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
14
B
N2
DG
6
1_555
hydrog
DG-DC PAIR
A
DG
4
A
N1
DG
4
1_555
B
DC
13
B
N3
DC
5
1_555
hydrog
DG-DG MISPAIR
A
DG
4
A
O6
DG
4
1_555
B
DG
14
B
N1
DG
6
1_555
hydrog
DC-DG PAIR
A
DC
5
A
N4
DC
5
1_555
B
DG
12
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
DC
11
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
DC
11
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
DC
11
B
N4
DC
3
1_555
hydrog
DG-DG MISPAIR
A
DG
6
A
N1
DG
6
1_555
B
DG
12
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
10
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
10
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
10
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N1
DA
8
1_555
B
DT
9
B
N3
DT
1
1_555
hydrog
WATSON-CRICK
A
DA
8
A
N6
DA
8
1_555
B
DT
9
B
O4
DT
1
1_555
DNA
DNA DUPLEX, GUANINE N2-GUANINE N2 INTERSTRAND CROSSLINK, DNA
1LUH
PDB
1
1LUH
1
8
1LUH
1
8
1LUH
A
1
1
8
9
16
1LUH
9
16
1LUH
B
1
1
8
BINDING SITE FOR RESIDUE TME B 1
B
TME
1
Software
4
A
DG
4
A
DG
4
4
1_555
A
DC
5
A
DC
5
4
1_555
B
DG
12
B
DG
4
4
1_555
B
DC
13
B
DC
5
4
1_555